If both are working and jetted properly it shouldn't cause problems, although if one is producing a lot more power than the other you would suffer vibration. Almost impossible to detect though, unless you want to two a dyno run for each cylinder with the cap of the other removed!
_________________
MC21SP Plaything
BMW F800GS Bumblebee
Triumph 9551 Daytona Big boys toy
FJ1100 Sporting relic
GTS1000 oddball